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Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules

Valentina Boeva1,2 email, Julien Clément3 email, Mireille Régnier2 email, Mikhail A Roytberg4,5 email and Vsevolod J Makeev1,6 email

Institute of Genetics and Selection of Industrial Microorganisms, GosNIIGenetika, 117545 Moscow, Russia

MIGEC, INRIA Rocquencourt, 78153 Le Chesnay, France

GREYC, CNRS UMR 6072, Laboratoire d'informatique, 14032 Caen, France

Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Puschino, Moscow Region, Russia

Puschino State University, Puschino, Moscow Region, Russia

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia

author email corresponding author email

Algorithms for Molecular Biology 2007, 2:13doi:10.1186/1748-7188-2-13

Published: 10 October 2007

Additional files

Additional file 1:

Bernoulli text model. Probability to find multiple occurrences of a single motif. The detailed description of the algorithm for the p-value calculation in the case of multiple occurrences of a single motif.

Format: PDF Size: 95KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 2:

Tree construction from PWM motif representation. The brief description of the procedure of the prefix tree construction from PWM motif representation.

Format: PDF Size: 102KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 3:

Tree construction from PWM motif representation. Steps of the prefix tree construction for a PWM and a given cut-off.

Format: BMP Size: 556KB Download file


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